Biol4559, Spring 2015

Bioinformatics and Functional Genomics

Suggested Texts

This course will cover topics in bioinformatics and programming. For the first half of the course, the Pevzner book (Bioinformatics and Functional Genomics (2nd ed) (2009) J. Pevzner, Wiley-Blackwell, ISBN:0470085851) will supplemental background, but the course will be skipping over the book. Although UVa library seems to think you can get this book online, it is not available. The book is on 3-hour reserver in the Brown Science and Engineering Library.

In addition, we will be introducing command line scripting with Python. The Haddock and Dunn book (Practical Computing for Biologists (2010) S. Haddock and C. Dunn, Sinauer, ISBN: 0878933913) is an oustanding introduction to many aspects of computing used in Biology. This book should be available on 3-hour reserve at the Brown Science and Engineering Library.

The second half of the course will focus on RNA-sequencing and gene expression analysis using 'R' and Bioconductor. These topics are not well covered by the Pevzner book (in the 2nd edition).

Students will less experience in command line scripting may also want to find a book with Unix commands.

Other books include:

Sequence Analysis

BIOINFORMATICS: Sequence and Genome Analysis, D. W. Mount (2004) Cold Spring Harbor Press ISBN 0-879-69712-1 Excellent, comprehensive text on sequence analysis, with new material on gene expression analysis. Highly recommended, but not required. (on reserve, HSL)

Bioinformatics for Dummies, J.-M. Claverie, C. Notredame (2003) Wiley ISBN 0-764-51696-5 Comprehensive mix of practical approaches

BIOINFORMATICS 2nd ed., A. D. Baxevanis and B. F. Ouellette (2001) Wiley-Interscience ISBN 0-471-38391-0 Excellent overview of databases and sequence analysis, stronger on "How To" than fundamentals. (on reserve, HSL)

Biological Sequence Analysis: Probabilistic Models Of Proteins And Nucleic Acids (1998) Durbin, Richard (Ed), Eddy, R., Krogh, A., Mitchison, G., Durbin, R., ISBN: 0-521-629-713 - Outstanding book on the statistical foundations of alignment and pattern finding methods, particularly Hidden Markov Models. Very mathematical.

Algorithms on strings, trees, and sequences : computer science and computational biology (1997) Dan Gusfield - Strong computer science orientation on algorithms.

Phylogenetic Methods

Fundamentals of Molecular Evolution 2nd ed Li and Graur (2000) Sinauer - Evolution is a much larger discipline that we can begin to cover in this course, but this book will be used for the evolution lectures, and it provides an excellent general background to phylogenetic methods and evolutionary problems in general. Recommended strongly. (on reserve, HSL)

Molecular Systematics 2nd ed. Hillis, Moritz, and Mable (eds) (1996) Sinauer - Excellent comprehensive overview of molecular phylogenetics. See Chapt. 11, Phylogenetic Inference for the a current review of methods and programs for constructing evolutionary trees.

Introduction to Molecular Biology

Recombinant DNA: Genes and Genomics: A Short Course Watson, Myers, Caudy, and Witkowski 3rd Edition, (2006) W. H. Freeman ISBN 0-716-72866-4 Amazon (on reserve, Brown Science and Engineering Library)

Introduction to Unix

Learning the UNIX Operating System O'Reilly & Associates - Excellent quick introduction to unix. Contains many short examples that should be tried.

Learning GNU Emacs O'Reilly & Associates - To get the most out of this course, and the Unix computers, you MUST learn a Unix text editor, and emacs is a power choice. This is an excellent introduction that covers the most common emacs commands in 100 pages.

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